1. Read in a tree and estimate all subtrees of that tree. Store the subtrees as an object.

2. Calculate a distance metric from your tree to each one of the subtrees. The phangorn library (and others) will calculate the standard bipartition distance (Robinson-Foulds) between pairs of trees; if there is a distance of zero from your tree to one of the subtrees, you know that your tree is identical in branching structure to that subtree.